update to match what the DIH JS function does, but folded into the regular processing
updates for status fields
Merge branch 'master' of https://github.com/mpi2/PhenotypeArchive

# By jwgwarren (1) and mrelac (1)
# Via mrelac
* 'master' of https://github.com/mpi2/PhenotypeArchive:
  First cut at IndexerManager command-line option processing. Wrote IndexerManagerTest junit test.
  removed some logging from PipelineIndexer